Mercurial > repos > rnateam > splitfasta

diff splitFasta.py @ 0:bc25ba9d9fcf draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hacked/splitFasta commit fcd6ef7e59971abd6b6a3a5401f92bcdef6ef76c
author rnateam
date Sun, 05 Jul 2015 08:37:52 -0400
parents
children ae4d5733272f
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/splitFasta.py	Sun Jul 05 08:37:52 2015 -0400
@@ -0,0 +1,14 @@
+import sys, os
+if __name__ == "__main__":
+    #assuming perfect input, read every two lines
+    inpath = sys.argv[1]
+    file_contents = open(inpath, 'r').readlines()
+    os.makedirs('splits')
+    inname = os.path.basename(inpath)
+    for i in range(0, len(file_contents), 2):
+        headline = file_contents[i]
+        outname = headline[1:headline.index(' ')]+'.fa'
+        outfile = open(os.path.join('splits',outname), 'w')
+        outfile.write(file_contents[i])
+        outfile.write(file_contents[i+1])
+        outfile.close()