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Added a clustal test file, an example notebook, and alignment parsing… #1

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76 changes: 76 additions & 0 deletions examples/test.clustal
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Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,76 @@
CLUSTAL O(1.2.4) multiple sequence alignment


mouse MMPPWLLARTLIMALFFSCLTPGSLNPCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDL
opossum -MVPWMVMALIMATTFFSCPDPGSCHSCLEVFPSIEYQCMDQNFSKVPMDIPASTQKLDL
* **:: :: : **** *** : *:**.*.* ******::**** ***:**:::**

mouse SFNPLKILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGS
opossum SFNPLRSLAPRSFSRITELRILDLSRCDIQKIEDDTYEGLHNLSTLILTGNPIQSLGIRA
*****: * ***.::**: ******:*:.***.::.***:**.**********:. :

mouse FSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVD
opossum FYGLPKLQKLVVVETNLMSLEDFPIGHIITLQELHLGHNSISSLQLPSYFASFSSMKHLD
* ** .*::**.***:* ***.****::***::*::.** * * :**:**:.::.: *:*

mouse LSYNYIQTITVNDLQFLRENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSN
opossum LHLNQIKNISDGDLEPVKLNPN--LTLDLSENPIQYIHPGAFKGIHLSGLKLRSSFHNST
* * *:.*: .**: :: **: *:**:* ***::*: **:**:* *.**..*:.*.

mouse IMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDD-I
opossum IMEACIKGMTGLKVGKLVLGNYKNDIQMTSFESSILDGLCEVDIGEFRMVQPSQFPSDGN
**::*::.::**:* :*:**::*:: :: ** **::***:* *.***:. .:* .*

mouse VKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQLKQ---FPTLDLPFLKSLTL
opossum GVFKCLVNVSVLFLVNTDIDQLTNLPIFPKLFSLSLTDCNFDIMPDLPSISLPSLKELKV
*:**.***.: *....*. * ::* . * ***: *::. :*::.** **.*.:

mouse TMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANF
opossum THHKDLTTLSDLALPNLQILDLSKNSLNVLSCCSDKTFNTPNLKYLNLSYNAHISLSKNF
* :*. ::..:***.*. ****:*:*.. .*** . :.* .*::*:**:*. * :* **

mouse MGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKM
opossum MGLENLESLDLQHTILKDHDKYPAFYSLINLRYLDISYTNTHVKFKNIFTGMSNLKHLKM
****:*: **:**: ** :: ** ** :* *********::.*..** *::.*: ***

mouse AGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSS
opossum AGSSFQDNILHDIFKNLTKLVSLNISYCQLERVSQETMSPLHQLQVLDLSHNKLQTFDPF
**.**:** * ::* * *:*. *::* ****::* .:. **:**:*::***:* :*

mouse HYNQLYSLSTLDCSFNRIETSKG-ILQHFPKSLAFFNLTNNSVACICEHQKFLQWVKEQK
opossum ICMPLLNLQVLNCSSNSITALNGENLQELSRTLISIDLSDNPFDCVCDHQIFFQWVKEHT
* .*..*:** * * : :* **.: ::* ::*::* . *:*:** *:*****:.

mouse QFLVNVEQMTCATPVEMNTSLVLDFNNSTCYMYKTIISVSVVSVIVVSTVAFLIYHFYFH
opossum HLLNRSKPMTCQTPSHMKDISVQLFDDSTCHMKKTVIAVSLLGIIVILLVLALVYKFYFH
::* . : *** ** .*: * *::***:* **:*:**::.:**: * *:*:****

mouse LILIAGCKKYSRGESIYDAFVIYSSQNEDWVRNELVKNLEEGVPRFHLCLHYRDFIPGVA
opossum LMLLAGCKNIGGGESIYDAFVIYSSQDEDWVRKELVKNLEEGVPSFQLCLHYRDFIPGVA
*:*:****: . **************:*****:*********** *:*************

mouse IAANIIQEGFHKSRKVIVVVSRHFIQSRWCIFEYEIAQTWQFLSSRSGIIFIVLEKVEKS
opossum IAANIIQEGFHKSRKVIVVISEHFIQSRWCKFEYEIAQTWQFLSSQAGIIFIILQKVEKS
*******************:*.******** **************::*****:*:*****

mouse LLRQQVELYRLLSRNTYLEWEDNPLGRHIFWRRLKNALLDGKASNPEQTAEEEQETATWT
opossum LLRQQMELYRLLNRNTYLEWEDTNLGRHVFWRRLRKALLDGRTKNPKGAAEEEFSQPVSP
*****:******.*********. ****:*****::*****::.**: :**** . .

mouse -
opossum T

CLUSTAL O(1.2.4) multiple sequence alignment


mouse MLPFILFSTLLSPILTESEKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGF
opossum MLQIVFFSILFTFTFTESMKNDWTCNSQDAEITYSSCDAKKPIPIININPCLSWRKTRGN
** :::** *:: :*** *::* ***.** *:** ** * *. :**: * *.*

mouse VHVEFIPRGNLKYLYFNLFISVN-SIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPF
opossum LSFYYVPRKDMKELYFNVHMELRSAIIVPKRKEVICRGVDDKYSFCRVLKGETINTTVPF
: . ::** ::* ****:.:.:. :* :******:*:* **.*****.*****:**::**

mouse SFEGILFPKGHYRCVAEAIAGDTEEKLFCLNFTIIHRRDVN
opossum SYSSLKFPKGLYIFIAEAFSGSTEDSMFCCNITLKLK----
*:..: **** * :***::*.**:.:** *:*: :
272 changes: 272 additions & 0 deletions examples/testing.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import phylopandas as phypd"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"seq_df = phypd.read_fasta(\"test.fasta\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style>\n",
" .dataframe thead tr:only-child th {\n",
" text-align: right;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: left;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>description</th>\n",
" <th>id</th>\n",
" <th>name</th>\n",
" <th>sequence</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5...</td>\n",
" <td>gi|2765658|emb|Z78533.1|CIZ78533</td>\n",
" <td>gi|2765658|emb|Z78533.1|CIZ78533</td>\n",
" <td>CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGA...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>gi|2765657|emb|Z78532.1|CCZ78532 C.californicu...</td>\n",
" <td>gi|2765657|emb|Z78532.1|CCZ78532</td>\n",
" <td>gi|2765657|emb|Z78532.1|CCZ78532</td>\n",
" <td>CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGA...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>gi|2765656|emb|Z78531.1|CFZ78531 C.fasciculatu...</td>\n",
" <td>gi|2765656|emb|Z78531.1|CFZ78531</td>\n",
" <td>gi|2765656|emb|Z78531.1|CFZ78531</td>\n",
" <td>CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGA...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>gi|2765655|emb|Z78530.1|CMZ78530 C.margaritace...</td>\n",
" <td>gi|2765655|emb|Z78530.1|CMZ78530</td>\n",
" <td>gi|2765655|emb|Z78530.1|CMZ78530</td>\n",
" <td>CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGA...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>gi|2765654|emb|Z78529.1|CLZ78529 C.lichiangens...</td>\n",
" <td>gi|2765654|emb|Z78529.1|CLZ78529</td>\n",
" <td>gi|2765654|emb|Z78529.1|CLZ78529</td>\n",
" <td>ACGGCGAGCTGCCGAAGGACATTGTTGAGACAGCAGAATATACGAT...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" description \\\n",
"0 gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5... \n",
"1 gi|2765657|emb|Z78532.1|CCZ78532 C.californicu... \n",
"2 gi|2765656|emb|Z78531.1|CFZ78531 C.fasciculatu... \n",
"3 gi|2765655|emb|Z78530.1|CMZ78530 C.margaritace... \n",
"4 gi|2765654|emb|Z78529.1|CLZ78529 C.lichiangens... \n",
"\n",
" id name \\\n",
"0 gi|2765658|emb|Z78533.1|CIZ78533 gi|2765658|emb|Z78533.1|CIZ78533 \n",
"1 gi|2765657|emb|Z78532.1|CCZ78532 gi|2765657|emb|Z78532.1|CCZ78532 \n",
"2 gi|2765656|emb|Z78531.1|CFZ78531 gi|2765656|emb|Z78531.1|CFZ78531 \n",
"3 gi|2765655|emb|Z78530.1|CMZ78530 gi|2765655|emb|Z78530.1|CMZ78530 \n",
"4 gi|2765654|emb|Z78529.1|CLZ78529 gi|2765654|emb|Z78529.1|CLZ78529 \n",
"\n",
" sequence \n",
"0 CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGA... \n",
"1 CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGA... \n",
"2 CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGA... \n",
"3 CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGA... \n",
"4 ACGGCGAGCTGCCGAAGGACATTGTTGAGACAGCAGAATATACGAT... "
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seq_df.head()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"align_df = phypd.read_clustal(\"test.clustal\")"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style>\n",
" .dataframe thead tr:only-child th {\n",
" text-align: right;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: left;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th></th>\n",
" <th>description</th>\n",
" <th>id</th>\n",
" <th>name</th>\n",
" <th>sequence</th>\n",
" <th>star</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th rowspan=\"2\" valign=\"top\">0</th>\n",
" <th>0</th>\n",
" <td>mouse</td>\n",
" <td>mouse</td>\n",
" <td>&lt;unknown name&gt;</td>\n",
" <td>MMPPWLLARTLIMALFFSCLTPGSLNPCIEVVPNITYQCMDQKLSK...</td>\n",
" <td>* **:: :: : **** *** : *:**.*.* ******::**...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>opossum</td>\n",
" <td>opossum</td>\n",
" <td>&lt;unknown name&gt;</td>\n",
" <td>-MVPWMVMALIMATTFFSCPDPGSCHSCLEVFPSIEYQCMDQNFSK...</td>\n",
" <td>* **:: :: : **** *** : *:**.*.* ******::**...</td>\n",
" </tr>\n",
" <tr>\n",
" <th rowspan=\"2\" valign=\"top\">1</th>\n",
" <th>0</th>\n",
" <td>mouse</td>\n",
" <td>mouse</td>\n",
" <td>&lt;unknown name&gt;</td>\n",
" <td>MLPFILFSTLLSPILTESEKQQWFCNSSDAIISYSYCDHLKFPISI...</td>\n",
" <td>** :::** *:: :*** *::* ***.** *:** ** * *...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>opossum</td>\n",
" <td>opossum</td>\n",
" <td>&lt;unknown name&gt;</td>\n",
" <td>MLQIVFFSILFTFTFTESMKNDWTCNSQDAEITYSSCDAKKPIPII...</td>\n",
" <td>** :::** *:: :*** *::* ***.** *:** ** * *...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" description id name \\\n",
"0 0 mouse mouse <unknown name> \n",
" 1 opossum opossum <unknown name> \n",
"1 0 mouse mouse <unknown name> \n",
" 1 opossum opossum <unknown name> \n",
"\n",
" sequence \\\n",
"0 0 MMPPWLLARTLIMALFFSCLTPGSLNPCIEVVPNITYQCMDQKLSK... \n",
" 1 -MVPWMVMALIMATTFFSCPDPGSCHSCLEVFPSIEYQCMDQNFSK... \n",
"1 0 MLPFILFSTLLSPILTESEKQQWFCNSSDAIISYSYCDHLKFPISI... \n",
" 1 MLQIVFFSILFTFTFTESMKNDWTCNSQDAEITYSSCDAKKPIPII... \n",
"\n",
" star \n",
"0 0 * **:: :: : **** *** : *:**.*.* ******::**... \n",
" 1 * **:: :: : **** *** : *:**.*.* ******::**... \n",
"1 0 ** :::** *:: :*** *::* ***.** *:** ** * *... \n",
" 1 ** :::** *:: :*** *::* ***.** *:** ** * *... "
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"align_df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"It might be nice to be able to name the alignments instead of having each alignment be multiindexed by a number but maybe that's not a huge issue."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.1"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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