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Automate common sam & bam conversions
Python
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README.mkdn

mergesam: Automate common sam & bam conversions

Mergesam is a a tool to save you some time when interconverting sam and bam formats. When was the last time you sorted a bam file and didn't immediately index it afterward? For that matter, when was the last time you didn't sort a bam file? Mergesam aims to have sensible defaults and flexible options, in order to streamline your path from sam to ready-to-use bam and back.

Default: merge, sort, and index.

A common pattern that I have encountered when manipulating sam and bam files is to merge several such files into one bam file, then sort that bam file, then index it. With the mergesam script, this becomes a single simple command:

mergesam.py -o output.bam input1.sam input2.sam input3.sam

The result is that output.bam is a sorted bam file, with an accompanying index file output.bam.bai. An equivalent series of shell commands is:

samtools view -h input1.sam > temp.sam
samtools view input2.sam >> temp.sam
samtools view input3.sam >> temp.sam
samtools view -ubS temp.sam > temp.bam
samtools sort temp.bam output
samtools index output.bam
rm temp.sam temp.bam

One could also implement it as a single pipeline, with no intermediate files:

{
    samtools view -h input1.sam
    samtools view input2.sam
    samtools view input3.sam
} | samtools view -ubS | samtools sort - output
samtools index output.bam

If you find yourself frequently writing code like the above while manipulating sam and bam files, you might want to use mergesam instead.

Fully pipe compliant

Mergesam will happily read from standard input and write to standard output. In fact, this is the default:

cat input.sam | mergesam.py > output.bam

You can also specify standard input and output explicitly:

cat input.sam | mergesam.py -o - - > output.bam

Unfortunately, when writing to standard output, it is impossible to index the resulting file, since mergesam does not know where the output file is (or even if one exists). So if you want indexing, use the -o option with a filename, not a dash.

By the way, mergesam will never send binary (bam) output directly to your terminal unless you ask it to, using the --force_bam_tty option. Binary data will only be sent to standard output if it has been redirected or piped into another command, so don't worry about clobbering your terminal by accident.

Variations: unsorted, unindexed, uncompressed

Since you usually want your bam files to be sorted and indexed, sorting and indexing are both enabled by default. If you don't want either, you can use the --nosort or --noindex flags (Note that using both is redundant, since sorting is a prerequisite for indexing.) There is also the --sortbyname flag, which corrseponds to samtools sort -n -- sorting by read name instead of reference coordinate. Lastly, you can output uncompressed bam with the --uncompressed option (but note that sorted bam output is always compressed).

Input format is detected automatically

If the input files are already bam files, the command is the same. Input file types are automatically detected:

mergesam.py -o output.bam input1.bam input2.bam input3.bam

In fact, even if input.bam was actually a sam file, the above command would still work. It looks at the contents of the file to figure out what format it is. The one exception to this rule is that standard input is always sam format, since one cannot detect the format of an input stream without losing some of the input in the process. If you need to pipe bam data into mergesam, you'll need to pass it through samtools view -h.

bam_producer_command | samtools view -h | mergesam.py -o output.bam

Specifying a reference

If the sam files have no headers, you'll need a reference:

mergesam.py -o output.bam input.bam -r reference.fa.fai

You can also supply the name of a fasta file, in which case the fasta index will automatically be created and used.

mergesam.py -o output.bam input.bam -r reference.fa

If you don't have permission to create the index file in the same directory as the fasta file, the index will be created in a temporary directory and deleted when the program is finished.

SAM output

To output sam instead of bam, just use the --sam flag:

mergesam.py --sam -o output.sam input.bam -r reference.fa

Note that sam output is neither sorted nor indexed. By default, the sam output includes the header. To suppress it, use --noheader.

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