readSAM

Reads and parses a sam file.

readSAM(SAMfile,header=False)

  • SAMfile /path/to/file.sam
  • header logical, if True, reads the header information
  • returns a pandas dataframe with the respective SAM columns: 'QNAME','FLAG','RNAME','POS','MAPQ','CIGAR','RNEXT','PNEXT','TLEN','SEQ','QUAL' and a list of the headers if header=True
>>> import AGEpy as age
>>> SAMdf=age.readSAM("sample1.sam")
>>> print SAMdf.head()

CIGAR  \
0  J00137:91:HJG75BBXX:6:1101:27458:1244    4     *         0    0       *   
1   J00137:91:HJG75BBXX:6:1101:2483:1226    4     *         0    0       *   
2   J00137:91:HJG75BBXX:6:1101:6593:1244   16    II  11210427  255  2S146M   
3   J00137:91:HJG75BBXX:6:1101:9293:1244    0     I  10433525  255    150M   
4  J00137:91:HJG75BBXX:6:1101:13271:1244   16   III   5277278  255    150M   

RNEXT PNEXT TLEN                                                SEQ  \
0     *     0    0  CCAAAATCAGTTACAAAAAAATTAAATATCGAGTTCCTCCCCCAGA...   
1     *     0    0  ACGTGACCGATGGTTGGCATGGCACGCATACCACGGAAGCGTCTGC...   
2     *     0    0  AACAACAGCAGCAGCAGATTTACCAAAGGTTCCCAGCAAGACTAAT...   
3     *     0    0  CTTGATTGTACTGCTGTGGTGGACCGCGTGGTCCTCCTTGTTGGTT...   
4     *     0    0  GGACATGATGATCATGGCCACGACTCTCATGGACATAGTCATGATC...   

                                              QUAL  
0  AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ...  
1  A-<AF7FF-AF-A<--F-7<FAA7FFF7-<-<F7JF---7--77J7...  
2  7-AA7JF)JJJF<--7FF--7--AAA--<A7<--<<A-7-A-<<FJ...  
3  AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ...  
4  JFFAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJ...

writeSAM

Writes a pandas dataframe with the respective SAM columns: 'QNAME','FLAG','RNAME','POS','MAPQ','CIGAR','RNEXT','PNEXT','TLEN','SEQ','QUAL' into a sam file.

writeSAM(sam, SAMfile, header=None)

  • sam pandas dataframe to be writen
  • SAMfile /path/to/file.sam
  • returns nothing
>>> import AGEpy as age
>>> age.writeSAM(SAMdf,"modified.sam")

SAMflags

Explains a SAM flag.

SAMflags(x)

  • x flag
  • returns complete SAM flag explanation
>>> import AGEpy as age
>>> print age.SAMflags(64)

["0: Read unpaired", "0: Read not mapped in proper pair", "0: Read mapped", "0: Mate mapped", "0: Read direct strand", "0: Mate direct strand", "1: First in pair", "0: First in pair", "0: Primary alignment", "0: Read passes platform/vendor quality checks", "0: Read is not PCR or optical duplicate", "0: Not supplementary alignment"]